Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/518ade584338d1e989efc6c2a97f8f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/518ade584338d1e989efc6c2a97f8f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/09ab92fd6d06dd30552109cbffc247/Sig_18_Blood.md.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/09ab92fd6d06dd30552109cbffc247/Sig_18_Blood.md.bam.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i Sig_18_Blood.md.bam --algo AlignmentStat Sig_18_Blood.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo Sig_18_Blood.sentieon.insert_size_metrics --algo QualDistribution Sig_18_Blood.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle Sig_18_Blood.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle Sig_18_Blood.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:164000001, elapsed 0.0s, est remaining 0.6s, peak mem 78MB, user 0.5s, sys 0.3s, output queue size 4
progress 10% @chr2:72000001, elapsed 0.1s, est remaining 0.6s, peak mem 78MB, user 0.8s, sys 0.9s, output queue size 5
progress 15% @chr2:241000001, elapsed 0.1s, est remaining 0.5s, peak mem 78MB, user 1.4s, sys 1.3s, output queue size 11
progress 20% @chr3:157000001, elapsed 0.1s, est remaining 0.5s, peak mem 78MB, user 1.9s, sys 1.6s, output queue size 8
progress 25% @chr4:117000001, elapsed 0.2s, est remaining 0.5s, peak mem 78MB, user 2.3s, sys 2.1s, output queue size 11
progress 30% @chr5:85000001, elapsed 0.2s, est remaining 0.4s, peak mem 78MB, user 2.8s, sys 2.6s, output queue size 15
progress 35% @chr6:65000001, elapsed 0.2s, est remaining 0.4s, peak mem 78MB, user 3.4s, sys 2.9s, output queue size 1
progress 40% @chr7:49000001, elapsed 0.3s, est remaining 0.4s, peak mem 78MB, user 4.0s, sys 3.5s, output queue size 12
progress 45% @chr8:79000001, elapsed 0.3s, est remaining 0.4s, peak mem 78MB, user 4.1s, sys 5.4s, output queue size 18
progress 50% @chr9:49000001, elapsed 0.4s, est remaining 0.4s, peak mem 78MB, user 4.2s, sys 7.7s, output queue size 24
progress 55% @chr10:83000001, elapsed 0.5s, est remaining 0.4s, peak mem 78MB, user 4.2s, sys 9.9s, output queue size 14
progress 60% @chr12:6000001, elapsed 0.6s, est remaining 0.4s, peak mem 78MB, user 4.3s, sys 12.2s, output queue size 19
progress 65% @chr13:34000001, elapsed 0.6s, est remaining 0.3s, peak mem 78MB, user 4.4s, sys 14.4s, output queue size 12
progress 70% @chr14:80000001, elapsed 0.7s, est remaining 0.3s, peak mem 78MB, user 4.5s, sys 16.6s, output queue size 11
progress 75% @chr15:100000001, elapsed 0.8s, est remaining 0.3s, peak mem 78MB, user 4.7s, sys 18.8s, output queue size 21
progress 80% @chr17:67000001, elapsed 0.9s, est remaining 0.2s, peak mem 78MB, user 4.8s, sys 20.9s, output queue size 17
progress 85% @chr20:41000001, elapsed 0.9s, est remaining 0.2s, peak mem 78MB, user 5.0s, sys 22.9s, output queue size 20
progress 90% @chrX:28000001, elapsed 1.0s, est remaining 0.1s, peak mem 96MB, user 6.0s, sys 24.0s, output queue size 114
progress 95% @chrY:53000001, elapsed 1.1s, est remaining 0.1s, peak mem 108MB, user 6.9s, sys 25.5s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.9s, est remaining 0.0s, peak mem 123MB, user 9.4s, sys 27.8s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: AlignmentStat InsertSizeMetricAlgo QualDistribution BaseDistributionByCycle MeanQualityByCycle
license: sentieon:Metrics=31
input file size: 52290604
reads: 1001133
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.317 user 13.950 sys 15.294 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.000 user 0.010 sys 1.873 real
idle: 80 calls 0.014 user 0.010 sys 50.529 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 129040384 mem 9.623 user 28.337 sys 2.921 real